Perhaps this blog post by Bas is worth a read? I'm not sure exactly what's causing the database sync script to wipe out your data, but this post explains the process so you might be able to figure it out from there.
Due to merging branchlines into a branchline for the conversion, the SQL script was generated. The script contains a drop (and create) of almost 100 tables and some attributes. After consulting Mendix, we have decided to fix this on database level by analysing the SQL script and creating backup/restore scripts per table/attribute.
Bug or development issue is not 100% clear, don't do a conversion and (parallel) development at the same time.